NYU Dataset

Sequencing Data Decodes the Architecture of the Varicella-Zoster Virus Transcriptome

UID: 10477
* Corresponding Author
Description

The data from this study displays the complexity of the varicella-zoster virus (VZV) transcriptome architecture. VZV causes varicella and reactivates later in life to cause herpes zoster. The VZV genome is known to produce multitudes of overlapping transcripts and distinct open reading frames (ORFs) have been studied as well. However, the architecture of the VZV transcriptome remains unknown. This study examined VZV transcriptome architecture by integrating multiple short-read RNA sequencing approaches with long-read direct RNA sequencing on RNA isolated from VZV-infected cells.

As a result of mapping of transcription start sites, splice junctions, and polyadenylation sites, they identified 136 distinct polyadenylated VZV RNAs that encode canonical ORFs, noncanonical ORFs, and ORF fusions. This dataset contains sequencing data, as well as supplementary data tied to the publication. The supplementary data includes several tables, which contains data for transcription start sites and cleavage and polyadenylation sites identified within the VZV genome, splice sites utilized during VZV transcription, the complete VZV reannotation, overview of sequencing data sets, and database of primers used in the study.

Subject of Study
Subject Domain
Keywords

Access

Restrictions
Free to All
Instructions
All sequencing data associated with this study are available at Sequence Read Archive (SRA) with BioProject. Analyzed data sets generated as part of this study are freely available at GitHub. All other data are available on PubMed Central (PMC) under Supplementary Materials.
Access via SRA

Sequencing data
Accession #: PRJEB38829

Access via GitHub

Analyzed data

Access via PMC

Other data
Accession #: PMC7542360

Associated Publications
Data Type
Equipment Used
Applied Biosystems 3130XL
Applied Biosystems 7500
Applied Biosystems StepOnePlus
BD FACSLyric
Bio-Rad ChemiDoc MP
Illumina NextSeq 550
ImmunoSpot S6 Ultimate UV
Oxford Nanopore MinION
Thermo Scientific NanoDrop
Zeiss LSM 700
Software Used
BBMap
bedtools
ContextMap v2.0
CPC 2.0
findPeaks
FLAIR v1.3
FlowJo
Guppy v3.2.2
ImmunoSpot
minimap2
SAMtools
TrimGalore
Grant Support
JP17H05816/MEXT KAKENHI
JP16H06429/MEXT KAKENHI
JP16K21723/MEXT KAKENHI
JP17K008858/JSPS KAKENHI
Takeda Science Foundation/Takeda Science Foundation
Daiichi Sankyo Foundation/Daiichi Sankyo Foundation
022.005.032/NWO
University College London Hospitals Biomedical Research Centre/National Institute for Health Research
High Performance Computing Core/NYU Langone Health